Variant report

Variant	rs2571009
Chromosome Location	chr18:44650279-44650280
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:44648921..44650562-chr18:44675973..44678048,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167220	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11663321	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12953864	0.80[YRI][hapmap]
rs12960378	0.85[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12960444	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12963648	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12964465	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13381713	0.82[YRI][hapmap]
rs16954921	0.83[YRI][hapmap]
rs16954999	0.83[YRI][hapmap]
rs2251948	0.82[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2277717	0.84[AMR][1000 genomes]
rs2289133	0.83[YRI][hapmap]
rs2461247	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2571001	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2571016	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576030	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576031	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2576053	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2576056	0.82[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2576060	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2635040	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2635041	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2635042	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2635043	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2635045	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2635046	0.96[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2635047	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2635049	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2635050	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2668758	0.84[YRI][hapmap]
rs2668761	0.83[YRI][hapmap]
rs2684818	0.82[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2684820	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2684822	1.00[ASN][1000 genomes]
rs2684825	0.82[ASN][1000 genomes]
rs2684826	0.82[ASN][1000 genomes]
rs28693565	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28702976	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2932126	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3816125	0.85[CEU][hapmap];0.83[JPT][hapmap];0.86[EUR][1000 genomes]
rs7242978	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7504798	0.85[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9304341	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9960264	0.85[CEU][hapmap];0.83[JPT][hapmap];0.87[EUR][1000 genomes]
rs9961383	0.84[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv9629	chr18:44264693-44757511	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv833640	chr18:44552276-44714872	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv909612	chr18:44560875-44681485	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv576819	chr18:44602249-44677627	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv909613	chr18:44644530-44690107	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:44620800-44675400	Weak transcription	A549	lung
2	chr18:44621600-44674400	Weak transcription	Small Intestine	intestine
3	chr18:44624200-44654200	Weak transcription	Fetal Heart	heart
4	chr18:44626600-44664800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr18:44629200-44675800	Weak transcription	HUVEC	blood vessel
6	chr18:44630600-44660400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr18:44632000-44654200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr18:44632400-44675800	Weak transcription	Stomach Mucosa	stomach
9	chr18:44636200-44670600	Weak transcription	Pancreas	Pancrea
10	chr18:44636600-44661000	Weak transcription	Psoas Muscle	Psoas
11	chr18:44638400-44660800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr18:44639200-44662400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr18:44639600-44660600	Weak transcription	NHLF	lung
14	chr18:44639600-44665000	Weak transcription	Colonic Mucosa	Colon
15	chr18:44639600-44666400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr18:44639800-44654800	Weak transcription	HMEC	breast
17	chr18:44639800-44660600	Weak transcription	NH-A	brain
18	chr18:44639800-44660800	Weak transcription	Rectal Smooth Muscle	rectum
19	chr18:44640400-44662000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr18:44640600-44675600	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr18:44640800-44662000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr18:44641000-44653800	Weak transcription	HSMM	muscle
23	chr18:44641000-44654200	Weak transcription	Brain Anterior Caudate	brain
24	chr18:44641000-44654800	Weak transcription	Hela-S3	cervix
25	chr18:44641200-44654200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr18:44641200-44655600	Weak transcription	Fetal Brain Female	brain
27	chr18:44641200-44659600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr18:44641600-44654000	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr18:44641600-44654200	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr18:44641600-44654200	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr18:44641600-44660400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr18:44641600-44670400	Weak transcription	HepG2	liver
33	chr18:44641600-44674000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr18:44641600-44675800	Weak transcription	Lung	lung
35	chr18:44641800-44650800	Weak transcription	Fetal Stomach	stomach
36	chr18:44641800-44652400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr18:44641800-44653600	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr18:44641800-44653600	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr18:44641800-44653800	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr18:44641800-44653800	Weak transcription	Left Ventricle	heart
41	chr18:44641800-44654000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr18:44641800-44655000	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr18:44641800-44655800	Weak transcription	Brain Cingulate Gyrus	brain
44	chr18:44641800-44656200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr18:44641800-44660400	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr18:44641800-44660800	Weak transcription	Brain Substantia Nigra	brain
47	chr18:44641800-44661400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr18:44641800-44662000	Weak transcription	K562	blood
49	chr18:44641800-44662600	Weak transcription	Brain Angular Gyrus	brain
50	chr18:44641800-44663200	Weak transcription	Esophagus	oesophagus

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